Effluents from a small-scale free-surface flow constructed wetland, used for polishing of secondary treated wastewater, contained significantly higher concentrations of potentially viable Giardia duodenalis cysts and Enterocytozoon bieneusi spores than did wetland influents consisting of secondary treated wastewater. Zoonotic Assemblage A of G. duodenalis cysts was identified in wetland inflows, while Assemblage A and two nonhuman infective Assemblages (i.e., C, and E) were present in wetland effluents. E. bieneusi spores represented genotype K based on DNA sequencing analysis of internal transcribed spacer. The study demonstrated that: (1) free-surface flow small-scale constructed wetlands may not provide sufficient remediation for human zoonotic protozoa and fungi present in secondary treated wastewater; (2) dogs and livestock can substantially contribute human-pathogenic protozoan and fungal microorganisms to engineered vegetated wetland systems; and (3) large volumes of wetland effluents can contribute to contamination of surface waters used for recreation and drinking water abstraction and therefore represent a serious public health threat.